Barack Obama has authorised targeted air strikes against Islamic militants in Iraq, as the US military began an airborne operation to bring relief to thousands of minority Iraqis driven to a grim, mountain-top refuge.

Describing the threats against stranded Yazidi refugees as holding the potential for “genocide”, the president said he had authorised limited air strikes to help Iraqi forces, to assist in the fight to break the siege and protect the civilians trapped there.

“When we face a situation like we do on that mountain, with innocent people facing the prospect of violence on a horrific scale and we have a mandate to help - in this case a request from the Iraqi government - and when we have unique capabilities to act to avoid a massacre, I believe the United States cannot turn a blind eye,” the president said in a late-night statement from the White House.

“Earlier this week, one Iraqi said no-one is coming to help. Well, today America is coming to help,” he said.

The delivery of humanitarian relief, in the form of air drops by US jets, took place after a day of intense debate at the White House over how to respond to an Isis army that has caused mass civilian displacement as it moves closer to the previously stable Kurdistan region of Iraq.

The air drops represented the first aerial mission over Iraq since 2011 for a purpose beyond conducting surveillance on Isis, providing long-scheduled military sales or transporting the extra hundreds of US special operations “advisers” that Obama ordered into Iraq to help Baghdad confront the threat from Isis. They marked the start of the deepest American engagement in Iraq since US troops withdrew in late 2011 after nearly a decade of war.

The US military was already helping the Iraqi government co-ordinate air drops of vital supplies to at least 40,000 Iraqis, mostly from the Yazidi minority, trapped on top of Mount Sinjar in the northwest of Iraq after death threats from the Islamists who have overrun much of the region.

Iraqi and Kurdish officials on Friday said they welcomed the air drops and authorisation of air strikes. “We thank Barack Obama,” said Khalid Jamal Alber, of the Kurdish religious affairs ministry. “Kurdistan is the place for religious minorities.”

Qaraqosh, Iraq’s largest Christian city, was left all but abandoned as the jihadist group Islamic State (Isis) advanced through minority communities in the country’s north-west and towards the Kurdish stronghold of Irbil. Late on Thursday night the UN security council condemned the attacks and urged international support for the Iraqi government.

Obama said “targeted air strikes” could soon be used to protect American personnel in Irbil, and could also be used to protect Baghdad if it came under pressure. He claimed the steps were a necessary response to a deteriorating humanitarian situation, in which there were “chilling reports” of mass executions and the enslavement of Yazidi women.

“In recent days Yazidi women, men and children from the region of Sinjar have fled for their lives,” he said. “Thousands, perhaps tens of thousands are now hiding high up the mountain with little but the clothes on their backs, they are without food, they are without water. People are starving, children are dying of thirst. Meanwhile Isis forces below have called for the systematic destruction of the Yazidi people, which would constitute genocide.”

UN officials say an estimated 200,000 new refugees are seeking sanctuary in the Kurdish north from Islamic extremists who have pursued them since the weekend. Qaraqosh, south-east of Mosul and home to around 50,000 Christians, was the latest to fall, with most residents fleeing before dawn on Thursday as convoys of extremists drew near.

Other Christian towns near Mosul, including Tel Askof, Tel Keif and Qaramless, have also largely been emptied. Those who remained behind were reportedly given the same stark choice given to other minorities, including Yazidis: flee, convert to Islam or be killed.

Iraqi troops have concentrated on defending Baghdad and the Shia south, leaving the defence of minorities in the north to the Kurdish peshmurga. However, even the much vaunted Kurdish forces were no match for the heavy weapons wielded by the jihadists as they advanced in recent days.

Without any protection, Yazidis, Christians and Turkmen are being uprooted from communities they have lived in for millennia and the geo-social fabric of Iraq is being rapidly shredded.

The Chaldean archbishop of Kirkuk, Joseph Thomas, described the situation in northern Iraq as “catastrophic, a crisis beyond imagination”. He demanded urgent intervention to save what remained of the area’s Christian heritage.

Kurdish officials on Thursday demanded more help in catering for refugees. The Kurdish administered areas have seen staggering numbers cross their notional border since the original Isis onslaught two months ago. In the first week alone, some 500,000 people are thought to have fled towards Irbil.

The capital of the Kurdish north is already home to a new Chaldean Christian community, which fled Baghdad in the wake of an Isis-led massacre inside a cathedral in October 2010. Many fleeing Christians have headed for the Ainkawa neighbourhood, which is home to Baghdad’s Christian exiles.

The past 11 years of war and insurrection since the US invasion have led to most of Iraq’s Christians fleeing. Numbers have plummeted starkly from an estimated one million before 2003 to around 150,000 now. A large number of those who remain are now displaced.

Isis has threatened to redraw the unitary borders that were carved out of the ruins of the Ottoman empire. The group’s rampant insurgency and the inability of state actors to stop it has rendered the frontier between Iraq and Syria evermore irrelevant.

In the absence of central government authority, Shia militias are taking dominant roles, amplifying sectarian enmity between Islam’s two most dominant sects.

Iraq’s beleaguered prime minister, Nouri al-Maliki, no longer has the authority to unite the country’s disparate sects. Maliki, a Shia Muslim, had disenfranchised much of the country’s Sunni community over the past three years, some of whom have turned to Isis as a means of reasserting themselves.

After digging in for the past two months, Maliki now faces a desperate battle to form a government, with his key backer Iran understood to have told him that it no longer supports his bid to lead the country for a third term.

Massoud Barazani, a Kurdish leader, has said he is moving towards holding a referendum that could pave the way for an independence bid, a move that could spell the end of Iraq, and unsettle surrounding countries, including Syria, Turkey and Iran.

The UN security council warned that the Isis attacks could constitute crimes against humanity and that those responsible should be held accountable. “The members of the security council also urge all parties to stop human rights violations and abuses and ensure humanitarian access and facilitate the delivery of assistance to those fleeing the violence,” said Britain’s UN ambassador Mark Lyall Grant, reading from a statement after an emergency consultation requested by France.

White House officials made clear the more aggressive US posture was prompted by rapid Isil advances on Irbil on Wednesday but insisted in a conference call with reporters that Obama did not anticipate a “sustained campaign” against what they called a “sophisticated military force”.

There are already constant US air patrols over Irbil but the US has no plans to evacuate diplomats or military advisers in the city – believing it can keep any further advances at bay with air power alone.

As of Thursday night there had been no offensive air missions. The humanitarian mission involved C17 and C130 cargo planes dropping 5,300 gallons of water and 8,000 ready meals (MREs) intended to provide short-term assistance to 8,000 of the “many thousands” of refugees thought to be trapped on the mountain.

US officials confirmed they were expecting a new Iraqi prime minister to be appointed by Sunday, suggesting the White House believes its precondition for greater political unity in Iraq before military intervention can take place may be within sight.

The White House says it has been consulting with the US Congress over its intervention but does not believe it needs authorisation for military action and merely plans to file a report under the war powers act if air strikes go ahead. Obama’s authorisation for the Pentagon to carry out attacks is “geographically restricted to Iraq” and does not include Syria.

A Lockheed Martin factory in the US that manufactures Hellfire air-to-ground missiles has been operating seven days a week to provide weapons destined for Iraqi government and Kurdish forces under pre-existing support arrangements.